Sketchmap

docs/src/bibliography.rst

@@ -24,6 +24,18 @@ References
     by Machine Learning Datasets", Materials Cloud Archive 2019.0023/v2 (2019),
     https://doi.org/10.24435/materialscloud:2019.0023/v2.
 
+.. [Ceriotti2011]
+    Michele Ceriotti, Giovanni A. Tribello, and Michele Parrinello,
+    "Simplifying the representation of complex free-energy landscapes using
+    sketch-map", Proceedings of the National Academy of Sciences, 108(32),
+    13023-13028 (2011). https://doi.org/10.1073/pnas.1108486108
+
+.. [Ceriotti2013]
+    Michele Ceriotti, Giovanni A. Tribello, and Michele Parrinello,
+    "Demonstrating the transferability and the descriptive power of sketch-map",
+    Journal of Chemical Theory and Computation, 9(3), 1521-1532 (2013).
+    https://doi.org/10.1021/ct3010563
+
 .. [Helfrecht2020]
     Benjamin A Helfrecht, Rose K Cersonsky, Guillaume Fraux, and Michele Ceriotti,
     "Structure-property maps with Kernel principal covariates regression." 2020 Mach.

docs/src/conf.py

@@ -60,6 +60,7 @@
     "regression",
     "reconstruction",
     "neighbors",
+    "decomposition",
 ]
 sphinx_gallery_conf = {
     "filename_pattern": "/*",

docs/src/getting-started.rst

@@ -52,3 +52,17 @@ Notebook Examples
    :start-line: 4
 .. include:: examples/pcovc/index.rst
    :start-line: 4
+
+.. _getting_started-decomposition:
+
+Non-linear Dimensionality Reduction
+-----------------------------------
+
+.. automodule:: skmatter.decomposition
+   :noindex:
+
+Notebook Examples
+^^^^^^^^^^^^^^^^^
+
+.. include:: examples/decomposition/index.rst
+   :start-line: 4

docs/src/index.rst

@@ -82,6 +82,23 @@
                 </div>
                 </div>
             </div>
+            <div class="col-sm d-flex">
+                <div class="card text-center mb-4" style="background-color: transparent">
+                <div class="card-body">
+                    <h5 class="card-title" style="margin-top: 0px">
+
+.. only:: html
+
+  :ref:`getting_started-decomposition`
+
+.. raw:: html
+
+                    </h5>
+                    <p class="card-text">Non-linear dimensionality reduction using
+                    Sketch-map algorithm with transfer functions.</p>
+                </div>
+                </div>
+            </div>
         </div>
     </div>
     <br>

docs/src/references/decomposition.rst

@@ -70,3 +70,17 @@ Kernel PCovC
     .. automethod:: inverse_transform
     .. automethod:: decision_function
     .. automethod:: score
+
+.. _SketchMap-api:
+
+SketchMap
+---------
+
+.. autoclass:: skmatter.decomposition.SketchMap
+    :show-inheritance:
+    :special-members:
+
+    .. automethod:: fit
+    .. automethod:: transform
+    .. automethod:: fit_transform
+    .. automethod:: score

examples/decomposition/README.rst

@@ -0,0 +1,2 @@
+Decomposition
+=============